In North Carolina, massive flooding in the wake of Hurricane Matthew isolated or swamped these and other hog farms and their waste lagoons, raising fears of environmental contamination. (Arelis Hernández/The Washington Post)

NEW BERN, N.C. – A filthy brown sea, a slurry of mud, debris, chemicals and waste, has overtaken miles of rural counties in North Carolina. Against the drab water, the shiny metal roofs of hog houses are impossible to miss, visible from the air, as are the rectangular and diamond-shaped outlines of massive lagoons constructed just feet away.

When those lagoons are doing their job, the liquid excrement they hold is a deep reddish-pink. Berms and pumps are designed to keep that bacteria-laden sludge from spilling out. But across coastal plain here – home to one of the highest concentrations of hog farms in the country – the lagoons’ content now looks more like the surrounding floodwater.

In a state already reeling from lost lives, homes and livelihoods, the color is evidence of major environmental risks.

Friends and family of 83-year-old Carolyn Griffin are trying to convince her to evacuate her home after it was flooded in Seven Springs, N.C. (Dalton Bennett/The Washington Post)

Hundreds of hog and poultry farms may have been inundated last week as the Neuse, Lumber and Tar rivers roared over their banks, a rampage powered by the deluge of Hurricane Matthew. The carcasses of several thousand drowned hogs and several million drowned chickens and turkeys were left behind. An incalculable amount of animal waste was carried toward the ocean. Along the way, it could be contaminating the groundwater for the many people who rely on wells in this part of the state, as well as threatening the delicate ecosystems of tidal estuaries and bays.

The extent of the damage will not be known until the North Carolina Department of Environmental Quality conducts tests in the coming weeks. But it has quickly renewed criticism of industry practices and state regulation, particularly of the state’s 2,100 hog farms.

“What this flooding does is really bring to light all the human health and environmental consequences of letting them have these open pits of [fecal] waste just sitting out there,” said Mae Wu, an attorney with the Natural Resources Defense Council.

The North Carolina Pork Council, which considers its industry “among the most highly regulated” in the state’s agricultural sector, has been upbeat in the hurricane’s wake. After accusing its most vocal critic, the nonprofit advocacy group Waterkeepers Alliance, of having “deliberately exaggerated the environmental impact” from hog lagoons, it announced on Friday that there’d been zero waste pits breached and just 11 flooded.

The presence of mass-scale swine and poultry lots and processing plants in a sandy floodplain – a region once dotted by small tobacco farms – has long posed a difficult dilemma for a state where swine and poultry represent billions of dollars a year for the economy.

The sheer size of many operations is mind-boggling; the world’s biggest hog-processing plant, the Smithfield Foods facility located in the town of Tar Heel, slaughters 30,000 animals a day. In a statement, Smithfield said none of its farms had suffered “a lagoon failure” as of Thursday afternoon. “This remains a serious, life-threatening situation, and our top priorities continue to be the safety and well-being of our employees and the care of our animals,” the statement concluded.

During Hurricane Floyd in 1999, hog lagoons across the eastern part of North Carolina broke open and dumped tons of liquid and solid waste into the storm waters. That material flowed downstream, eventually settling in coastal estuaries. It was blamed for elevated nitrogen and phosphorous levels, algae blooms and fish kills, remembers Travis Graves, an environmental scientist and member of the Waterkeepers Alliance.

State environmental officials insist they learned lessons from Floyd. The previous year, the state had put a moratorium on building new farms with more than 250 hogs and expanding existing large farms. After the hurricane, it bought out 42 hog operations located in the floodplain, essentially removing 103 waste lagoons. Other lagoons were relocated to higher ground and, in some cases, re-engineered to withstand inundation.

Yet the effort remains unfinished, with “at least” 150 facilities that the state never closed, according to Michelle Nowlin, a professor of environmental law at Duke University. Many critics maintain that the moratorium contains loopholes that have long rendered the bill ineffective.

“What I do hope,” Nowlin stressed, “is that this serves as a wake-up call in the aftermath for regulatory officials and elected officials to say, we need to finish this job, and get these animals out of the floodplain.”

Steve Wing, an epidemiologist at the University of North Carolina, offers a more terse admonition. “Storing vast quantities of fecal waste in flood plains is a serious and preventable public health threat,” he said.

State officials are being circumspect. Donald van der Vaart, secretary of the Department of Environmental Quality, said that it is getting reports on impacted lagoons and that he is “cautiously optimistic” no breaches will occur. A breach is the worst-case scenario in which the berm surrounding the lagoon breaks and spills into the river not only bacteria-laden liquid but solid fecal waste.

Hurricane Floyd’s environmental impact in North Carolina was so severe in part because of the large number of hog lagoon breaches. Following Matthew, the department has counted 10 to 12 lagoons that were inundated, with floodwaters topping the berms and spreading diluted waste. Van der Vaart expects that number to rise.

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Incredible photos of floodwaters in North Carolina

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Rivers are rising to record crests in the state after more than 17 inches of rain fell during Hurricane Matthew.

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Rivers are rising to record crests in the state after more than 17 inches of rain fell during Hurricane Matthew.

Oct. 13, 2016Floodwaters associated with Hurricane Matthew surround a church sign and homes in Lumberton, N.C. Gov. Pat McCrory said Thursday the number of power outages was down to about 55,000, from a high of nearly 900,000 when the storm hit last week.Brian Blanco/AP

Once waters recede and more roads become passable, his agency will conduct in-person inspections. “It’s too early to send people out and get into these peoples’ businesses,” he said Saturday.

That’s why the “riverkeepers” have taken to the sky in recent days, to shoot photos and survey for themselves what Graves calls a toxic soup. They dismiss some officials’ explanations that the impact of the diluted waste will be “mitigated naturally” because of the volume of water that submerged the region.

Along the lower Neuse River alone, Rick Dove said he’s seen more than a dozen hog lagoons swamped. He thinks comparisons to Floyd are apt.

“As I’m flying, it’s almost like I’m back in time to 1999,” Dove said last week. “I flew Floyd just like I’m flying Hurricane Matthew. And I can tell you, its impact on the animal industry is almost identical.”

Graves, a passionate, ponytailed activist, was the riverkeeper in the air on Saturday, flying in a single-engine prop plane over Craven, Wayne, Lenoir and Greene counties. “Look to your right,” he said, signaling the pinkish-red pool below. “That is what it’s supposed to look like.”

But as the plane turned, a cluster of farms came into view, islands in the vast, dark flood water. The hog houses were inundated, and it was obvious their lagoons had been under water just a few hours prior. On a sliver of higher ground – the lone spot of green – a herd of cows huddled together to stay dry.

“That’s exactly what we were afraid of,” Graves said as he positioned his zoom lens out the window. “There’s no way that [lagoon] didn’t mix in with flood waters.”

Since the rivers began rising, Graves has been documenting the GPS coordinates of all the flooded lagoons and cross-referencing them to the master map he and others created to pinpoint farm locations. The group is collecting and compiling this data as part of a rapid response program, which dispatches environmental scientists and activists to document the impacts of the storm.

The Waterkeepers Alliance has another concern, too. To lower the risk of lagoon breaches, farmers may have sprayed the liquid waste onto surrounding fields, proactively.

“That is not the preferred method, obviously,” said van der Vaart, of the state environment quality agency, “but if we’re in a situation where the farmer is faced with either a structural threat on the integrity of the lagoon versus spraying the liquid, then the latter is preferred.”

It may be the lesser evil, but research suggests it’s a significant health risk nonetheless.

One recent study of North Carolina’s waterways found that dangerous bacteria like E. coli and fecal coliforms were significantly higher in water both upstream and downstream from factory hog farms and that spraying “can lead to off-site migration of swine fecal wastes.” In regions where hog farm density is high, it concluded, there is an “overall poor sanitary quality of surface waters.”

The environmental consequences of Hurricane Matthew could take weeks to realistically assess. Dove and other activists want the state to draw broader conclusions.

“The lesson that we should’ve learned with all the hurricanes coming through here – that these animal factories should not be in harm’s way – is one that we keep learning over and over and over again. And we have asked the governor to get these animal factories out of the flood plain and adjacent land to the flood plain, and they have refused.”

Hernández reported from New Bern, N.C., and Mooney and Fritz from Washington. Chico Harlan and Kirk Ross also contributed to this story from Raleigh, N.C.

Correction: A previous version of this story included before-and-after photos of a breached waste lagoon that was not associated with hogs. We have removed that photo.

Arelis R. HernándezArelis Hernández covers local politics in Prince George’s and regularly moonlights as a national breaking news reporter. She joined the Post in 2014 after nearly four years at the Orlando Sentinel. She most recently spent two months in Puerto Rico covering the aftermath of Hurricane Maria. Follow

Angela FritzAngela Fritz is an atmospheric scientist and The Washington Post's deputy weather editor. Before joining The Post, Fritz worked as a meteorologist at CNN in Atlanta and Weather Underground in San Francisco. She has a BS in meteorology and an MS in earth and atmospheric science. Follow

Chris MooneyChris Mooney covers climate change, energy, and the environment. He has reported from the 2015 Paris climate negotiations, the Northwest Passage, and the Greenland ice sheet, among other locations, and has written four books about science, politics and climate change. Follow